theislab/moscot

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Multi-omic single-cell optimal transport tools

Stars: 216
Forks: 16
Open beginner issues: 0
Indexed issues: 32
Avg merge: 16h 2m
Merged PRs (30d): 3

Dominant language: Python
License: BSD-3-Clause
Last GitHub push: Aug 25, 2026
Latest indexed: Sep 20, 2026
Contributing guide: Contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed

Beginner friendly Everything

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32 open issues indexed

GraphOTTOutput.transport_matrix returns the expanded (n+m)² matrix, not the (n, m) block Open

Difficulty 3/5 1-2 days Newbie friendliness 64/100

theislab/moscot#847 · Opened Aug 24, 2026
ott-jax incompatible with JAX >= 0.9 (is_vmappable removed) — online/batched OT broken Open

Difficulty 2/5 1-3 hours Newbie friendliness 68/100

theislab/moscot#842 · 1 comment · Opened Jun 5, 2026
Incorporating Biological Priors and integrating multiple dataset Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

theislab/moscot#841 · Opened Mar 20, 2026
Interpolation with moscot Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

theislab/moscot#840 · 1 comment · Opened Nov 30, 2025
Issue with Proportional Splitting in Sankey Diagram for RunX1ko Genotype Using MOSCOT Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

theislab/moscot#835 · 1 comment · Opened Jul 30, 2025
BirthDeathProblem.solve Error: tp1[8, 9].set_graph_xy(dfs[8, 9].astype("float"), t=100.0) Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

theislab/moscot#834 · 4 comments · Opened Jul 26, 2025
Add multi-GPU support Open

theislab/moscot#803 · 1 assignee · Opened Feb 24, 2025
Add reasonable ranges for hparams to user guide Open

theislab/moscot#781 · 1 assignee · Opened Jan 13, 2025
No error to check convergence in output of SpatioTemporalProblem Open

documentation examples

theislab/moscot#768 · 11 comments · 3 assignees · Opened Dec 5, 2024
Refactoring moscot to include moscot.neural Open

theislab/moscot#763 · 5 comments · 1 assignee · Opened Nov 7, 2024
Full rank initializers Open

theislab/moscot#734 · 1 comment · 1 assignee · Opened Jul 10, 2024
`.impute` consumes too much memory Open

theislab/moscot#729 · 5 comments · 1 assignee · Opened Jul 5, 2024
Refactor: Check if both x and x_callback is given Open

low-prio

theislab/moscot#715 · 2 comments · 1 assignee · Opened Jun 14, 2024
Unbalance FGW full rank marginal normalization issue Open

theislab/moscot#691 · 7 comments · 1 assignee · Opened Apr 30, 2024
Add examples for advanced data passing, e.g. how to pass `x_attr/y_attr` Open

theislab/moscot#643 · 2 comments · 1 assignee · Opened Jan 8, 2024
symbol column key argument when using gene sets Open

low-prio

theislab/moscot#608 · 1 comment · 1 assignee · Opened Sep 26, 2023
Add `.copy` method Open

low-prio

theislab/moscot#601 · 2 assignees · Opened Sep 5, 2023
Pull/push in a batch-wise fashion Open

theislab/moscot#592 · 3 comments · 2 assignees · Opened Aug 11, 2023
Jit the `apply` function Open

theislab/moscot#577 · 1 assignee · Opened Jul 10, 2023
Unify the way `push/pull` results are saved. Open

theislab/moscot#576 · 1 assignee · Opened Jul 10, 2023
Batch-wise computation of gene imputation. Open

enhancement

theislab/moscot#569 · 1 assignee · Opened Jun 26, 2023
Make resolution of sankey strips a variable Open

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

theislab/moscot#527 · Opened Apr 16, 2023
get same output when pulling/pushing a vector on problem level or solution level Open

conceptual

theislab/moscot#518 · 2 assignees · Opened Apr 6, 2023
Add names of base methods in corresponding problem classes Open

documentation

theislab/moscot#513 · 1 assignee · Opened Apr 4, 2023
Simplify/improve typing Open

low-prio

Difficulty 4/5 3-5 days Newbie friendliness 25/100

theislab/moscot#491 · Opened Mar 10, 2023
Fix tests Open

test

Difficulty 3/5 1-2 days Newbie friendliness 35/100

theislab/moscot#489 · Opened Mar 10, 2023
Better tutorial/example structure Open

documentation

Difficulty 5/5 Over a week Newbie friendliness 25/100

theislab/moscot#488 · Opened Mar 10, 2023
Conventional commits/release notes Open

low-prio

theislab/moscot#487 · 1 assignee · Opened Mar 10, 2023
Push/pull plotting when no categories are passed fails Open

bug

theislab/moscot#475 · 1 assignee · Opened Feb 17, 2023
Examples to be written Open

documentation

theislab/moscot#403 · 5 comments · 2 assignees · Opened Nov 7, 2022
remove generic types Open

low-prio

theislab/moscot#304 · 1 comment · 1 assignee · Opened Oct 14, 2022
Improve generating/saving regression test files Open

theislab/moscot#239 · 1 assignee · Opened Jun 13, 2022

theislab/moscot

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